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[bioontology-support] A Bug Report and Two Questions

Anders Riutta anders.riutta at gladstone.ucsf.edu
Tue Oct 28 15:07:50 PDT 2014


Another issue: I am trying to submit a new ontology for the WikiPathways vocabulary [3], but when I choose the acronym "wikipathways", I get the following error:

Errors On Form
acronym_value_validator : The acronym value wikipathways is invalid

Thanks.
Anders

[3] http://vocabularies.wikipathways.org/wp


----- Original Message -----
> From: "Anders Riutta" <anders.riutta at gladstone.ucsf.edu>
> To: "Paul R Alexander" <palexander at stanford.edu>
> Cc: support at bioontology.org
> Sent: Tuesday, October 28, 2014 2:20:40 PM
> Subject: Re: [bioontology-support] A Bug Report and Two Questions
> 
> Hi Paul,
> 
> Thanks for the response. I went to the URL at [1], but it took me to a page
> with the message "The page you are looking for wasn't found. Please try
> again." Changing "&t=mappings" to  "#mappings" as in [2] gave me a list of
> mappings, but I don't see an option for deleting. There is just a button to
> "Create New Mapping".
> 
> Anders
> 
> [2]
> https://bioportal.bioontology.org/ontologies/BP?p=classes&conceptid=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Control#mappings
> 
> 
> ----- Original Message -----
> > From: "Paul R Alexander" <palexander at stanford.edu>
> > To: "Anders Riutta" <anders.riutta at gladstone.ucsf.edu>
> > Cc: support at bioontology.org
> > Sent: Monday, October 27, 2014 4:14:03 PM
> > Subject: Re: [bioontology-support] A Bug Report and Two Questions
> > 
> > Thanks for reporting the problems with projects. These have now been fixed.
> > 
> > To delete the mapping, you can go to the class page for the class you have
> > mapped [1] and there should be a checkbox and button for deleting.
> > 
> > We do not have data available in SKOS, but you can get the mapping data per
> > ontology using our REST API and convert as needed. For example,
> > http://data.bioontology.org/ontologies/BRO/mappings
> > <http://data.bioontology.org/ontologies/BRO/mappings>. Documentation on
> > using the REST API is here: http://data.bioontology.org/documentation
> > <http://data.bioontology.org/documentation>
> > 
> > Please let me know if you have other questions.
> > 
> > Paul
> > 
> > [1]
> > https://bioportal.bioontology.org/ontologies/BP?p=classes&conceptid=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Control&t=mappings
> > <https://bioportal.bioontology.org/ontologies/BP?p=classes&conceptid=http://www.biopax.org/release/biopax-level3.owl#Control&t=mappings>
> > 
> > 
> > > On Oct 22, 2014, at 12:04 PM, Anders Riutta
> > > <anders.riutta at gladstone.ucsf.edu> wrote:
> > > 
> > > Hello,
> > > 
> > > Thanks for making the BioPortal available. It's a great resource. I have
> > > one bug report and two questions.
> > > 
> > > Bug Report: When I try to access projects, I get the following error:
> > > 
> > >  "We're sorry but something has gone wrong. We have been notified of this
> > >  error."
> > > 
> > >  This happens both when I'm logged in
> > >  <https://bioportal.bioontology.org/projects?user=http%3A%2F%2Fdata.bioontology.org%2Fusers%2Fariutta>
> > >  and when I'm not <http://bioportal.bioontology.org/projects>.
> > > 
> > > Question 1: How do I delete a mapping I created? I added the following
> > > mapping, but it's not exactly correct, so I would like to delete it.
> > > Also,
> > > it appears to be duplicated
> > >  Control (BP) <=> stimulation (SBO)
> > >  REST Mapping 08/17/2014 by ariutta
> > > 
> > > Question 2: Can I bulk download the mapping data in SKOS format?
> > > 
> > > Thanks.
> > > Anders Riutta
> > > Gladstone Institutes
> > > _______________________________________________
> > > bioontology-support mailing list
> > > bioontology-support at lists.stanford.edu
> > > https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> > 
> > 
> 


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